As of now, villages can tend to be a little powerful, even when you first recruit them (as i've let my opinion be known..heh)
One suggestion that i'd have would be to mess with the distribution %'s to make things more challenging, for example:

Goblin before upgrade: 50% goblin, 50% rat
Spider Den before upgrade: 60% Spider, 40% rat
Hydra: Maybe add a weaker creature to take the place of hydras until upgraded
and so on...

2) Along with this, you could add a new meta spell to upgrade this ratio. Perhaps you could have a decent amount of upgrades in order to upgrade the numbers up to were they'd max. say...

This could help balance the game a bit, while making more use of meta-mana in a way that is arguably simplistic enough to not complicate things, but give a little extra spice to the decision making.

I got this idea while testing different villages in a certain area. Sometimes, I found a goblin village could be way overpowered simply by generating the full roster of goblins (12 out of 12), as opposed to a mix of goblins and rats (6/6 or even 4/8rats ), which would be a more appropriate composition, considering how many creatures you get.

If you wanted something simpler, you could simply scale back the spawn ratio, and have the advanced training do 2 things:
1)increase unit amount (but to something like 25% more rather then 50% more...50% just clutters the battlefield up)
2)Adjust the ratio to a more favorable one (so 80% goblin and 20% rat in the goblin village as an example)

Along with this, I'd add 2 or 3 spells in which you can upgrade a totem so that you could still keep your villages handy for defending locations if need be.

Regarding a frame of reference to use when trying to balance villages this way, I would look at the offline singleplayer realms.
The Gravelings & Goblins realm would be particularly handy as it has:

An elf in range of mana flux
spider lair in range of citadel
2 elf villages near a palace

If you were to utilize these villages before attacking a strategic point, it becomes that click and drag fest where you start and end the match by dragging your 6 creatures across the map to wipe out the lord.

Creating a balance, were at least saving up these many creatures has more of a consequence could incentivize not waiting for the whole village to generate before leaving. (again, upgrades could be factored in as well)

again, for defending a location, giving spell totems more spells to defend themselves can balance the lack of troops out. The spells work perfectly as a balancer as they don't spawn with the player's wizard, so you can easily isolate the balance of them to accommodate for the 2 different scenarios (i.e 1)attacking something w/ wizard + villages 2) defending a strategic location after the wizard has gone too far to help them.

Recruiting villages and rallying them to help a wizard fight decreases realm score as you wait. Using villages to take out a lord on their own often fails at even higher chances to win via auto-roll. The most critical defensive use of a village is recruiting early to defend an early key resource like a Mana Flux. If the player is too deep in the realm and the mana flux defenders lose to a marauder that often ends a realm run. Any realm run ended by a village auto-roll is a bitter defeat. Increasing the probability that villagers fail to defend the early mana flux decreases relevance of the player in a run failure outcome. It can waste over an hour or more of an otherwise splendid realm run. Integrating villages into realm win-conditions typically increases the grind of a realm rather than decrease it. Meta-spell tier upgrades don't come online until #1 - mana flux seizure and #2 - wizard is in a citadel after taking the mana flux and #3 - village is still relevant to upgrade. Very often the earlier villages will be most needed at their weakest and less needed when there is opportunity to upgrade: The Upgrade Paradox.

In cases where villages are required to beat lords due to a wizard taboo I've seen goblins or dwarves with around 14% chance to win. It happens because sometimes the lord sitting on a taboo is flush with elite units. Even a 60% chance to beat a lord sitting on a taboo is often going to fail enough to end a realm run, especially if it involves villages slower to rally. Goblins are not reliable to win and terrible to rely on for defending key resources. Also, 5 rats and 1 goblin happens. The ratios you present for distribution % actually decrease village variance and strengthen villages despite putting a ceiling on their strength. Decent goblin distribution % is hardly worse than better, but 4-5 rats is pathetic. Scaling back spawn rates eliminates recruiting of elite villages. They are just too slow to justify the risk even at improved chance to win. Already, 2 giant rallies is about the max # of tries before too much banishment time is wasted. Even a typical 65% giant chance to win is terrible in a series of 2 tries.

One promising change that would create an alternative to Auto-Roll Hell is to fix Invite a Friend / Invite an Ally for village battles. It increases player interaction and provides a wizard to face the opposing wizard. Wizard-taboo protected resources would still require an auto-roll for villages to win an assault. Since village battles show Invite a Friend / Invite an Ally as options before fighting a villager battle I assume it was meant to be in the game. Maybe auto-rolls weren't supposed to end so many realm runs..

I like village-centric realms for their part in quest narratives and giving realms character. I like villages as options to assist tough assaults, optional fortification of key resources/bottlenecks or playing the kudos game of razing one to recruit another. Tying villages to win-dependent auto-roll situations involves dynamics such as player relevance that are important when considering adjustments to village strengths.

I like the idea of fixing village/ally options. This would be fun, as well as give the player a helping hand when they need it. Although, it'd be nice to have the game balanced to the extent that you aren't reliant on other players helping you when the game doesn't give you options to work the problem out on your own.

The trick is trying to balance these 2 scenarios:

1)When a village is first recruited
2)After a village receives advanced training
3)When 2 villages get combined

in 1), the village tends to be either:
-Really overpowered when combined with a wizard.
-Best off just auto-resolving when on its own.

in 2), the village tends to be either:
-Overpowered when combined with a wizard to the extent that you're just simply clicking stuff until the opponent is dead.
-Pretty decent as a defense for a location, depending on the village type (with the exception of dwarf settlements; they're fairly silly in this context due to the 1 movement limit of them all)

in 3), the villages tend to be fairly robust. I feel like the 6+ spells that a totem can gain access to tends to hit that sweet spot. I feel like the way villages are intended is to give totems only an advantage so far as starting troops are concerned. I feel that if you were able to balance the villager number with the total spells you allowed a village that you might find a sweet spot with all of the number generation (which would save you from doing something like slowing down spawn rates of villages)

Ultimately, I think the villages should be balanced to the point were auto-resolve is not a preferred option. The only reason that I think players would use auto-resolve is because:
1) The lord is just simply too hard to imagine beating with a village troop (factors like having a single undead reinforcement can do enough to chokepoint a whole roster of villages)
2) It's just boring, which i believe can be mainly attributed to the lack of balance. It generally falls under being too weak or too strong, which takes away all of the tension.

All of this said, I did have an idea that involved using kudos to upgrade "the amount of troops a village was willing to send out" which would cause you to balance your use of kudos more. This kudos thing wouldn't impact how many troops spawned in the event of a marauder attacker so it might sort the balancing act inbetween the dynamic of "battles with wizard + villagers" and "battles with totem + villagers" Ultimately, it'd just force a bit more discretion on the player when choosing which villages to recruit and upgrade.

--------------------------------------
*Another idea
Everything said, I'm wondering if having the option to get a total of 6 spells might just work this out. My rational here would be that the player would be given the choice on whether to upgrade their village via spells or with troops. In some contexts, having a tier 1 village with 8 spells would be handier than a tier 2 village with 3 spells (being they'd both cost 25 mana)

Perhaps having the option the tier of villages in smaller incriments could allow a decent combination of both.

The village upgrade paradox undercuts efforts to moderate the cost of upgrading villages. If mana fluxes could be restricted to a finite supply of mana then realm designers could include them early so players have choices about boosting their villages or using mana to explore, etc. but without so much mana that players receive too much advantage. Also, when a mana flux is finite then a player only has to guard it with a village until the flux is exhausted which makes it easier to defend. It did just occur to me that if fluxes were finite that would mean fluxes towarrds the end would need to be large enough in supply to still be useful to the player. As long as realm designer can set fluxes to infinite supply that could suffice for fluxes towards the end of the realm.

I think we're crossing over from realm design into gameplay discussion btw.